ScientificPython is a collection of Python modules that are useful for
scientific applications. Most of them need the Numerical Python
extension (aka NumPy), which is available from SourceForge; see
http://numpy.sourceforge.net for details.

This is release 2.9 of ScientificPython. The odd minor release number
indicates a development release.

All the documentation is in Doc. To browse the reference manual for all
the modules, point your browser at Doc/Reference/index.html.

If you find bugs, please tell me, and if you improve something, please
send me the modified version. I don't promise anything, but since I
use these modules a lot for my own work, I have an interest in keeping
them bug-free and usable.

For updates, check

  http://dirac.cnrs-orleans.fr/ScientificPython/

from time to time.


Konrad Hinsen
Centre de Biophysique Moléculaire (CNRS)
et Synchrotron Soleil
E-Mail: hinsen@cnrs-orleans.fr

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Installation:
-------------

Required: Python 2.5 or higher. Most modules also require Numerical
Python. If you want to use the netCDF interface module, you also need
the netCDF library, version 3.0 or higher.

1) Unix-like systems, including Linux and MacOS X

Installation is as simple as

    python setup.py build
    python setup.py install

(the second command requires root privileges on many installations).
This will build the netCDF module if it can find a netCDF installation
in either /usr/local or in /usr. If your netCDF installation is elsewhere,
set the environment variable "NETCDF_PREFIX" to the directory in which
"include/netcdf.h" and "lib/netcdf.so" are located.

2) Windows

To build the netCDF interface module, you must have a binary version
of netCDF. You can either compile it yourself, or download the
precompiled netcdf.dll from the netCDF Web site. You also need the
file netcdf.h, which you can find in the netCDF source code
distribution. PLEASE MAKE SURE THAT NETCDF.DLL AND NETCDF.H ARE FOR
THE SAME NETCDF RELEASE!

Installation is as simple as

    python setup.py build --netcdf_prefix=dir_h --netcdf_dll=dir_dll
    python setup.py install --netcdf_prefix=dir_h --netcdf_dll=dir_dll

where "dir_h" is the directory in which netcdf.h is located and
"dir_dll" is the the directory in which netcdf.dll is located.

Alternatively, you can create a binary installer using

    python setup.py bdist_wininst --netcdf_prefix=dir_h --netcdf_dll=dir_dll



Using numpy or numarray:
------------------------

There are three nearly compatible implementations of numeric arrays for
Python: the original one, Numerical Python (module name "Numeric"),
a later rewrite called numarray, and an evolution of Numeric that integrates
features from numarray, called numpy.

Scientific Python was written for Numeric and still uses Numeric by
default. However, it is possible to use numpy or numarray instead of Numeric
for all array operations. To do this, use

    python setup.py build --numpy
    python setup.py install

or

    python setup.py build --numarray
    python setup.py install

for installation.

Note that this is a new feature and not very well tested. Feedback is welcome.
Note also that the modules

  Scientific.Functions.Derivatives
  Scientific.Functions.FirstDerivatives
  Scientific.Functions.LeastSquares

do not work correctly with numarray because they rely on a feature of
Numeric/numpy that is missing in numarray. For the same reason, the modules

  Scientific.Functions.Interpolation
  Scientific.Physics.PhysicalQuantities

can be used only partially with numarray, the application of mathematical
functions to the defined objects does not work.

In the long run, numpy is likely to replace both Numeric and numarray.
At some point, ScientificPython will thus use numpy by default.

---------------------------------------------------------------------------

Examples:
---------

The directory Examples provides a few simple example applications,
including a C extension module that uses the netCDF C-API.


Using Scientific.Visualization.VMD under Windows
------------------------------------------------

If VMD is installed in its default location, everything should work
fine automatically. Otherwise, an error message will be printed. The
default location is

	c:\Program Files\University of Illinois\VMD\vmd.exe

or its equivalent on non-English Windows versions ("Program Files"
changes its name).
